diff --git a/CellDesigner-plugin/pom.xml b/CellDesigner-plugin/pom.xml
index 1f0c13239d63c1e767d1ad4ee0b51d3e9ea00a93..9fd4b4804fc1d55ec1f16a709265b076cca6c49d 100644
--- a/CellDesigner-plugin/pom.xml
+++ b/CellDesigner-plugin/pom.xml
@@ -1,85 +1,87 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>parent</artifactId>
- <version>1.0</version>
- </parent>
- <artifactId>CellDesigner-plugin</artifactId>
- <!-- dependency from the MapViewer model -->
-
- <repositories>
- <repository>
- <id>central</id>
- <url>http://repo.maven.apache.org/maven2/</url>
- </repository>
-
- <repository>
- <id>repo</id>
- <releases>
- <enabled>true</enabled>
- <checksumPolicy>ignore</checksumPolicy>
- </releases>
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <url>file://${project.basedir}/repo</url>
- </repository>
-
- </repositories>
-
-<build>
- <plugins>
- <plugin>
- <artifactId>maven-assembly-plugin</artifactId>
- <executions>
- <execution>
- <id>make-assembly</id> <!-- this is used for inheritance merges -->
- <phase>package</phase> <!-- bind to the packaging phase -->
- <goals>
- <goal>single</goal>
- </goals>
- <configuration>
- <descriptor>install.xml</descriptor>
- </configuration>
- </execution>
- </executions>
- </plugin>
- </plugins>
-</build>
-
-
- <dependencies>
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>model</artifactId>
- <version>1.0</version>
- </dependency>
-
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>commons</artifactId>
- <version>1.0</version>
- </dependency>
-
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>converter-CellDesigner</artifactId>
- <version>1.0</version>
- </dependency>
-
- <dependency>
- <groupId>jp.sbi</groupId>
- <artifactId>celldesigner</artifactId>
- <version>${celldesigner.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.sbml</groupId>
- <artifactId>libsbml</artifactId>
- <version>${libsbml.version}</version>
- </dependency>
-
- </dependencies>
-
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>parent</artifactId>
+ <version>1.0</version>
+ </parent>
+ <artifactId>CellDesigner-plugin</artifactId>
+ <!-- dependency from the MapViewer model -->
+
+ <repositories>
+ <repository>
+ <id>central</id>
+ <url>http://repo.maven.apache.org/maven2/</url>
+ </repository>
+
+ <repository>
+ <id>repo</id>
+ <releases>
+ <enabled>true</enabled>
+ <checksumPolicy>ignore</checksumPolicy>
+ </releases>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <url>file://${project.basedir}/repo</url>
+ </repository>
+
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <executions>
+ <execution>
+ <id>make-assembly</id> <!-- this is used for inheritance merges -->
+ <phase>package</phase> <!-- bind to the packaging phase -->
+ <goals>
+ <goal>single</goal>
+ </goals>
+ <configuration>
+ <descriptor>install.xml</descriptor>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+
+ <dependencies>
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>commons</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter-CellDesigner</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>jp.sbi</groupId>
+ <artifactId>celldesigner</artifactId>
+ <version>${celldesigner.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.sbml</groupId>
+ <artifactId>libsbml</artifactId>
+ <version>${libsbml.version}</version>
+ </dependency>
+
+ </dependencies>
+
</project>
\ No newline at end of file
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index 3e36ff93a7dfd29fa2b27891fd6b556f29564dee..71357a911e75b274d81f18d5ec3762930216f72c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -160,7 +160,11 @@ public class RestAnnotationParser extends XmlParser {
return "";
}
} else if (value instanceof String) {
- return type.getCommonName() + ": " + value + "\n";
+ if (!((String) value).trim().isEmpty() || forceFullInfo) {
+ return type.getCommonName() + ": " + value + "\n";
+ } else {
+ return "";
+ }
} else if (value instanceof Integer) {
return type.getCommonName() + ": " + value + "\n";
} else if (value instanceof Collection) {
@@ -350,7 +354,7 @@ public class RestAnnotationParser extends XmlParser {
logger.debug("Y");
notes = notes.substring(notes.indexOf("</head>") + "</head>".length());
}
- notes = notes.replace("xmlns=\"http://www.w3.org/1999/xhtml\"","");
+ notes = notes.replace("xmlns=\"http://www.w3.org/1999/xhtml\"", "");
return notes.replaceAll("&", "&");
}
diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml
index 02b7787a01428db97df5cacda80e28901a87825f..f2d8e21147b738460e70b20d49b36325b4afd80d 100644
--- a/converter-sbml/pom.xml
+++ b/converter-sbml/pom.xml
@@ -76,9 +76,9 @@
<dependency>
<groupId>org.sbml.jsbml</groupId>
<artifactId>jsbml</artifactId>
- <version>1.3.1</version>
+ <version>${jsbml.version}</version>
<!-- for now we use lower version of log4j and this one introduce some
- problem with tomcat loggin -->
+ problem with tomcat logging -->
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
@@ -97,24 +97,67 @@
<artifactId>slf4j-api</artifactId>
</exclusion>
<exclusion>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
</exclusion>
<exclusion>
- <groupId>commons-logging</groupId>
- <artifactId>commons-logging</artifactId>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
</exclusion>
<exclusion>
- <groupId>org.codehaus.woodstox</groupId>
- <artifactId>stax2-api</artifactId>
+ <groupId>org.codehaus.woodstox</groupId>
+ <artifactId>stax2-api</artifactId>
+ </exclusion>
+ <!-- https://github.com/sbmlteam/jsbml/issues/156 -->
+ <exclusion>
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml-core</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
+ <dependency>
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml-core</artifactId>
+ <version>${jsbml.version}</version>
+ <!-- for now we use lower version of log4j and this one introduce some
+ problem with tomcat logging -->
+ <exclusions>
+ <exclusion>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-core</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-api</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-1.2-api</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-api</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.codehaus.woodstox</groupId>
+ <artifactId>stax2-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
- <groupId>org.codehaus.woodstox</groupId>
- <artifactId>stax2-api</artifactId>
- <version>${stax2-api.version}</version>
+ <groupId>org.codehaus.woodstox</groupId>
+ <artifactId>stax2-api</artifactId>
+ <version>${stax2-api.version}</version>
</dependency>
<dependency>
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
index 656622664598424d68d2630690ad8ad7b96b7b5f..be31323ace489bad052aa2171c8e6c23b4ffdfd4 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
+import java.awt.Color;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
@@ -11,6 +12,13 @@ import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.render.ColorDefinition;
+import org.sbml.jsbml.ext.render.LocalRenderInformation;
+import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.render.RenderConstants;
+import org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin;
+import org.sbml.jsbml.ext.render.RenderGroup;
+import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -116,6 +124,13 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
this.layout = layout;
}
+ protected RenderLayoutPlugin getRenderPlugin() {
+ if (layout.getExtensionCount() > 0) {
+ return (RenderLayoutPlugin) layout.getExtension("render");
+ }
+ return null;
+ }
+
protected lcsb.mapviewer.model.map.model.Model getMinervaModel() {
return minervaModel;
}
@@ -132,4 +147,47 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
return sbmlGlyphByElementId.get(elementId);
}
+ protected ColorDefinition getColorDefinition(Color color) {
+ RenderLayoutPlugin renderPlugin = getRenderPlugin();
+
+ LocalRenderInformation renderInformation = null;
+ for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
+ if (lri.getId().equals("minerva_definitions")) {
+ renderInformation = lri;
+ }
+ }
+ if (renderInformation == null) {
+ renderInformation = new LocalRenderInformation("minerva_definitions");
+ renderPlugin.addLocalRenderInformation(renderInformation);
+ }
+
+ for (ColorDefinition cd : renderInformation.getListOfColorDefinitions()) {
+ if (cd.getValue().equals(color)) {
+ return cd;
+ }
+ }
+ ColorDefinition colorDefinition = new ColorDefinition("color_" + colorToString(color), color);
+
+
+ renderInformation.addColorDefinition(colorDefinition);
+ return colorDefinition;
+ }
+
+ protected void assignStyleToGlyph(AbstractReferenceGlyph speciesGlyph, LocalStyle style) {
+ RenderGraphicalObjectPlugin rgop = new RenderGraphicalObjectPlugin(speciesGlyph);
+ rgop.setObjectRole(style.getRoleList().get(0));
+
+ speciesGlyph.addExtension(RenderConstants.shortLabel, rgop);
+ }
+
+ protected LocalStyle createStyle(T element) {
+ LocalRenderInformation renderInformation = new LocalRenderInformation();
+ LocalStyle style = new LocalStyle();
+ style.getRoleList().add("style_" + element.getElementId());
+ style.setGroup(new RenderGroup());
+ renderInformation.addLocalStyle(style);
+ getRenderPlugin().addLocalRenderInformation(renderInformation);
+ return style;
+ }
+
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
index e9926b9ed964c70c306b33fe2b0caf118b08006f..0103895ce8d9c39eba6e27eeebb632ea152a3d2d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
@@ -1,6 +1,9 @@
package lcsb.mapviewer.converter.model.sbml;
+import java.awt.Color;
+import java.util.HashMap;
import java.util.HashSet;
+import java.util.Map;
import java.util.Set;
import javax.xml.stream.XMLStreamException;
@@ -9,6 +12,9 @@ import org.apache.log4j.Logger;
import org.sbml.jsbml.AbstractNamedSBase;
import org.sbml.jsbml.Annotation;
import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.render.LocalRenderInformation;
+import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
@@ -89,4 +95,67 @@ public class SbmlBioEntityParser extends XmlParser {
return (idCounter++) + "";
}
+ /**
+ * Returns {@link LocalStyle} from the layout data identified by objectRole.
+ *
+ * @param objectRole
+ * object role identifier
+ * @return {@link LocalStyle} from the layout data
+ */
+ protected LocalStyle getStyleForRole(String objectRole) {
+ RenderLayoutPlugin renderPlugin = (RenderLayoutPlugin) layout.getExtension("render");
+ for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
+ for (LocalStyle style : lri.getListOfLocalStyles()) {
+ if (style.getRoleList().contains(objectRole)) {
+ return style;
+ }
+ }
+ }
+ return null;
+ }
+
+ protected Color getColorByColorDefinition(String fill) {
+ RenderLayoutPlugin renderPlugin = (RenderLayoutPlugin) layout.getExtension("render");
+ for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
+ if (lri.getColorDefinition(fill) != null) {
+ return lri.getColorDefinition(fill).getValue();
+ }
+ }
+ return null;
+ }
+
+ protected LocalStyle getStyleForElement(BioEntity element) {
+ LocalStyle result = getStyleByRole("style_" + element.getElementId());
+ if (result == null && element.getElementId().contains("__")) {
+ result = getStyleByRole("style_" + element.getElementId().split("__")[1]);
+ }
+ if (result == null) {
+ result = getStyleByRole("default_" + element.getClass().getSimpleName());
+ }
+ return result;
+ }
+
+ private Map<String, LocalStyle> styleById = null;
+
+ LocalStyle getStyleByRole(String string) {
+ if (styleById == null) {
+ styleById = new HashMap<>();
+ if (layout != null) {
+ RenderLayoutPlugin renderPlugin = (RenderLayoutPlugin) layout.getExtension("render");
+ if (renderPlugin != null) {
+ for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
+ if (lri.getId().equals("minerva_definitions")) {
+ for (LocalStyle style : lri.getListOfLocalStyles()) {
+ for (String role : style.getRoleList()) {
+ styleById.put(role, style);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return styleById.get(string);
+ }
+
}
\ No newline at end of file
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
index 6b2433971b351a52284b593e2af65136fe2a083f..4a4db0e0817b9a721a7cce99ed792ec6f7e59b94 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
@@ -6,6 +6,8 @@ import org.sbml.jsbml.ext.layout.BoundingBox;
import org.sbml.jsbml.ext.layout.Dimensions;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.Point;
+import org.sbml.jsbml.ext.render.ColorDefinition;
+import org.sbml.jsbml.ext.render.LocalStyle;
import lcsb.mapviewer.model.map.species.Element;
@@ -25,8 +27,14 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
dimensions.setWidth(element.getWidth());
dimensions.setHeight(element.getHeight());
boundingBox.setDimensions(dimensions);
-
speciesGlyph.setBoundingBox(boundingBox);
+
+ LocalStyle style = createStyle(element);
+ ColorDefinition color = getColorDefinition(element.getColor());
+ style.getGroup().setFill(color.getId());
+
+ assignStyleToGlyph(speciesGlyph, style);
+
}
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
index bac6ee8c1366bd7bf3fac869ed70a06f089bc067..0f9972fd83a2d9f993b9b9b4515a6296126ed638 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
+import java.awt.Color;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
@@ -12,6 +13,9 @@ import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.render.RenderConstants;
+import org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -57,6 +61,13 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
elementBySbmlId.put(species.getElementId(), species);
}
+ for (Element element : elements) {
+ LocalStyle style = getStyleForElement(element);
+
+ if (style != null) {
+ applyStyleToElement(element, style);
+ }
+ }
for (Pair<String, AbstractReferenceGlyph> idGlyphPair : getGlyphs(sbmlLayout)) {
String id = idGlyphPair.getLeft();
Element source = elementBySbmlId.get(id);
@@ -68,12 +79,7 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
if (glyph.getId() == null || glyph.getId().equals("")) {
throw new InvalidInputDataExecption("Glyph for Species " + idGlyphPair.getLeft() + " doesn't have id");
}
- Element elementWithLayout = source.copy();
- elementWithLayout.setElementId(glyph.getId());
- elementWithLayout.setX(glyph.getBoundingBox().getPosition().getX());
- elementWithLayout.setY(glyph.getBoundingBox().getPosition().getY());
- elementWithLayout.setWidth(glyph.getBoundingBox().getDimensions().getWidth());
- elementWithLayout.setHeight(glyph.getBoundingBox().getDimensions().getHeight());
+ Element elementWithLayout = createElementWithLayout(source, glyph);
minervaModel.addElement(elementWithLayout);
result.add(elementWithLayout);
elementBySbmlId.put(id, elementWithLayout);
@@ -91,6 +97,33 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
return result;
}
+ private Element createElementWithLayout(Element source, AbstractReferenceGlyph glyph)
+ throws InvalidInputDataExecption {
+ Element elementWithLayout = source.copy();
+ elementWithLayout.setElementId(glyph.getId());
+ elementWithLayout.setX(glyph.getBoundingBox().getPosition().getX());
+ elementWithLayout.setY(glyph.getBoundingBox().getPosition().getY());
+ elementWithLayout.setWidth(glyph.getBoundingBox().getDimensions().getWidth());
+ elementWithLayout.setHeight(glyph.getBoundingBox().getDimensions().getHeight());
+
+ RenderGraphicalObjectPlugin rgop = (RenderGraphicalObjectPlugin) glyph.getExtension(RenderConstants.shortLabel);
+ if (rgop != null) {
+ LocalStyle style = getStyleForRole(rgop.getObjectRole());
+ if (style == null) {
+ throw new InvalidInputDataExecption("Style " + rgop.getObjectRole() + " is not defined");
+ }
+ applyStyleToElement(elementWithLayout, style);
+ }
+ return elementWithLayout;
+ }
+
+ private void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
+ if (style.getGroup().getFill() != null) {
+ Color backgroundColor = getColorByColorDefinition(style.getGroup().getFill());
+ elementWithLayout.setColor(backgroundColor);
+ }
+ }
+
protected abstract List<Pair<String, AbstractReferenceGlyph>> getGlyphs(Layout sbmlLayout);
protected abstract Element parse(T species, Model sbmlModel) throws InvalidInputDataExecption;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 15a7771f0d8d8b857fc7f17653389615308ffa98..5501b2aa09c79d1dac5d6183f08ce41a30ffe711 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -11,6 +11,8 @@ import org.sbml.jsbml.SBMLWriter;
import org.sbml.jsbml.ext.layout.Dimensions;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.sbml.jsbml.ext.render.GlobalRenderInformation;
+import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionExporter;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
@@ -19,6 +21,7 @@ import lcsb.mapviewer.model.map.species.Species;
public class SbmlExporter {
Logger logger = Logger.getLogger(SbmlExporter.class);
+
public String toXml(lcsb.mapviewer.model.map.model.Model model)
throws SBMLException, XMLStreamException, InconsistentModelException {
SBMLDocument doc = new SBMLDocument(3, 1);
@@ -47,7 +50,7 @@ public class SbmlExporter {
return stream.toString();
}
- private Layout createSbmlLayout(lcsb.mapviewer.model.map.model.Model model, Model result) {
+ public Layout createSbmlLayout(lcsb.mapviewer.model.map.model.Model model, Model result) {
LayoutModelPlugin layoutPlugin = new LayoutModelPlugin(result);
Layout layout = new Layout();
Dimensions dimensions = new Dimensions();
@@ -64,6 +67,15 @@ public class SbmlExporter {
layout.setDimensions(dimensions);
layoutPlugin.add(layout);
result.addExtension("layout", layoutPlugin);
+
+ createSbmlRenderPlugin(layout, result);
return layout;
}
+
+ RenderLayoutPlugin createSbmlRenderPlugin(Layout layout, Model result) {
+ RenderLayoutPlugin renderPlugin = new RenderLayoutPlugin(layout);
+ renderPlugin.setRenderInformation(new GlobalRenderInformation());
+ layout.addExtension("render", renderPlugin);
+ return renderPlugin;
+ }
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index d27a540db2645e38c6ccc9e281537959ae20898b..7472ee1cbb776bfb8d42484d2f335210ff00e461 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -19,6 +19,7 @@ import org.sbml.jsbml.SBMLReader;
import org.sbml.jsbml.ext.SBasePlugin;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.sbml.jsbml.ext.render.LocalStyle;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
@@ -114,14 +115,15 @@ public class SbmlParser implements IConverter {
if (sbmlModel.getRuleCount() > 0) {
throw new NotImplementedException("Rule not implemented for model");
}
- createLayout(model, layout, params.isSizeAutoAdjust());
+ createLayout(model, layout, params.isSizeAutoAdjust(), reactionParser);
return model;
} catch (XMLStreamException e) {
throw new InvalidInputDataExecption(e);
}
}
- private void createLayout(Model model, Layout layout, boolean resize) throws InvalidInputDataExecption {
+ private void createLayout(Model model, Layout layout, boolean resize, SbmlReactionParser parser)
+ throws InvalidInputDataExecption {
if (model.getWidth() == null) {
double maxY = 0;
double maxX = 0;
@@ -150,6 +152,15 @@ public class SbmlParser implements IConverter {
try {
if (bioEntitesRequiringLayout.size() > 0) {
new ApplySimpleLayoutModelCommand(model, bioEntitesRequiringLayout, true).execute();
+ for (BioEntity bioEntity : bioEntitesRequiringLayout) {
+ if (bioEntity instanceof Reaction) {
+ LocalStyle style = parser.getStyleForElement(bioEntity);
+
+ if (style != null) {
+ parser.applyStyleToReaction((Reaction) bioEntity, style);
+ }
+ }
+ }
}
} catch (CommandExecutionException e) {
throw new InvalidInputDataExecption("Problem with generating layout", e);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
index 20e89b58a1a204cf0ade7042639e4a4be93e0326..28b6c80aff8c4317fa08c8b37f6f6ee7981323d7 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
@@ -23,6 +23,8 @@ import org.sbml.jsbml.ext.layout.Point;
import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
+import org.sbml.jsbml.ext.render.ColorDefinition;
+import org.sbml.jsbml.ext.render.LocalStyle;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.Configuration;
@@ -173,8 +175,8 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
}
@Override
- protected void assignLayoutToGlyph(Reaction reaction, AbstractReferenceGlyph compartmentGlyph) {
- ReactionGlyph reactionGlyph = (ReactionGlyph) compartmentGlyph;
+ protected void assignLayoutToGlyph(Reaction reaction, AbstractReferenceGlyph glyph) {
+ ReactionGlyph reactionGlyph = (ReactionGlyph) glyph;
boolean firstReactant = true;
reactionGlyph.setCurve(new Curve());
@@ -242,6 +244,14 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
modifierGlyph.setRole(SpeciesReferenceRole.MODIFIER);
}
}
+
+ LocalStyle style = createStyle(reaction);
+ ColorDefinition color = getColorDefinition(reaction.getReactants().get(0).getLine().getColor());
+ style.getGroup().setStrokeWidth(reaction.getReactants().get(0).getLine().getWidth());
+ style.getGroup().setFill(color.getId());
+
+ assignStyleToGlyph(reactionGlyph, style);
+
}
private void addOperatorLineToGlyph(ReactionGlyph reactantGlyph, NodeOperator operator, boolean reverse) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index add9c0916d66da509def9f93bd209fee8a9841b4..e02e9b12d4db8b66bb0682cc4a806c63d91666e2 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.sbml.reaction;
+import java.awt.Color;
import java.awt.geom.Point2D;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
@@ -22,6 +23,9 @@ import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
+import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.render.RenderConstants;
+import org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -41,6 +45,7 @@ import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
import lcsb.mapviewer.model.map.modifier.Inhibition;
import lcsb.mapviewer.model.map.modifier.Modulation;
import lcsb.mapviewer.model.map.modifier.Trigger;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.AndOperator;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
@@ -56,8 +61,6 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlReactionParser extends SbmlBioEntityParser {
Logger logger = Logger.getLogger(SbmlReactionParser.class);
- Layout layout;
-
lcsb.mapviewer.model.map.model.Model minervaModel;
ElementUtils eu = new ElementUtils();
@@ -108,33 +111,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
for (SpeciesReferenceGlyph speciesRefernceGlyph : glyph.getListOfSpeciesReferenceGlyphs()) {
SpeciesGlyph speciesGlyph = layout.getSpeciesGlyph(speciesRefernceGlyph.getSpeciesGlyph());
ReactionNode minervaNode = null;
- Class<? extends ReactionNode> nodeClass = null;
- if (speciesRefernceGlyph.getRole() != null) {
- switch (speciesRefernceGlyph.getRole()) {
- case ACTIVATOR:
- nodeClass = Trigger.class;
- break;
- case INHIBITOR:
- nodeClass = Inhibition.class;
- break;
- case PRODUCT:
- nodeClass = Product.class;
- break;
- case SIDEPRODUCT:
- nodeClass = Product.class;
- break;
- case SIDESUBSTRATE:
- nodeClass = Reactant.class;
- break;
- case SUBSTRATE:
- nodeClass = Reactant.class;
- break;
- case UNDEFINED:
- case MODIFIER:
- nodeClass = null;
- break;
- }
- }
+ Class<? extends ReactionNode> nodeClass = getReactionNodeClass(speciesRefernceGlyph);
if (reactionWithLayout.isReversible() && (nodeClass == Reactant.class || nodeClass == Product.class)) {
nodeClass = null;
@@ -233,6 +210,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
operator.setLine(line);
reactionWithLayout.addNode(operator);
}
+ assignRenderDataToReaction(glyph, reactionWithLayout);
+
minervaModel.addReaction(reactionWithLayout);
} catch (InvalidArgumentException e) {
throw new InvalidInputDataExecption(e);
@@ -255,6 +234,63 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
}
+ private Class<? extends ReactionNode> getReactionNodeClass(SpeciesReferenceGlyph speciesRefernceGlyph) {
+ Class<? extends ReactionNode> nodeClass = null;
+ if (speciesRefernceGlyph.getRole() != null) {
+ switch (speciesRefernceGlyph.getRole()) {
+ case ACTIVATOR:
+ nodeClass = Trigger.class;
+ break;
+ case INHIBITOR:
+ nodeClass = Inhibition.class;
+ break;
+ case PRODUCT:
+ nodeClass = Product.class;
+ break;
+ case SIDEPRODUCT:
+ nodeClass = Product.class;
+ break;
+ case SIDESUBSTRATE:
+ nodeClass = Reactant.class;
+ break;
+ case SUBSTRATE:
+ nodeClass = Reactant.class;
+ break;
+ case UNDEFINED:
+ case MODIFIER:
+ nodeClass = null;
+ break;
+ }
+ }
+ return nodeClass;
+ }
+
+ private void assignRenderDataToReaction(ReactionGlyph glyph, Reaction reactionWithLayout)
+ throws InvalidInputDataExecption {
+ RenderGraphicalObjectPlugin rgop = (RenderGraphicalObjectPlugin) glyph.getExtension(RenderConstants.shortLabel);
+ if (rgop != null) {
+ LocalStyle style = getStyleForRole(rgop.getObjectRole());
+ if (style == null) {
+ throw new InvalidInputDataExecption("Style " + rgop.getObjectRole() + " is not defined");
+ }
+ applyStyleToReaction(reactionWithLayout, style);
+ }
+ }
+
+ public void applyStyleToReaction(Reaction reactionWithLayout, LocalStyle style) {
+ if (style.getGroup().getFill() != null) {
+ Color color = getColorByColorDefinition(style.getGroup().getFill());
+ for (AbstractNode node : reactionWithLayout.getNodes()) {
+ node.getLine().setColor(color);
+ }
+ }
+ if (style.getGroup().getStrokeWidth() != null) {
+ for (AbstractNode node : reactionWithLayout.getNodes()) {
+ node.getLine().setWidth(style.getGroup().getStrokeWidth());
+ }
+ }
+ }
+
private PolylineData getLineFromReferenceGlyph(SpeciesReferenceGlyph speciesRefernceGlyph) {
PolylineData line = null;
for (CurveSegment segment : speciesRefernceGlyph.getCurve().getListOfCurveSegments()) {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
index c59f7cab22f89ef245becebd0ab8885d062121bd..2e9a90faca7c22117648dcd96573563c91a1bb0a 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
@@ -12,6 +12,7 @@ import lcsb.mapviewer.converter.model.sbml.species.AllSbmlSpeciesTests;
AllSbmlSpeciesTests.class, //
GenericSbmlParserTest.class, //
GenericSbmlToXmlParserTest.class, //
+ SbmlBioEntityExporterTest.class, //
SbmlExporterTest.class, //
SbmlPareserForInvalidReactionTest.class, //
SbmlParserTest.class, //
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..471f844b462f960b4d52d25e611d80b584f1f6e9
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java
@@ -0,0 +1,61 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import java.awt.Color;
+
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.sbml.jsbml.ext.render.ColorDefinition;
+import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
+
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class SbmlBioEntityExporterTest {
+
+ @Test
+ public void testEmptyGetRenderPlugin() {
+ @SuppressWarnings("rawtypes")
+ SbmlBioEntityExporter exporter = Mockito.mock(SbmlBioEntityExporter.class, Mockito.CALLS_REAL_METHODS);
+ Layout layout = new Layout();
+ exporter.setLayout(layout);
+
+ assertNull(exporter.getRenderPlugin());
+ }
+
+ @Test
+ public void testGetRenderPluginWithLayout() {
+ SbmlBioEntityExporter<?, ?> exporter = createMockExporter();
+ assertNotNull(exporter.getRenderPlugin());
+ }
+
+ @SuppressWarnings("rawtypes")
+ private SbmlBioEntityExporter createMockExporter() {
+ SbmlBioEntityExporter exporter = Mockito.mock(SbmlBioEntityExporter.class, Mockito.CALLS_REAL_METHODS);
+
+ SBMLDocument doc = new SBMLDocument(3, 1);
+ Model result = doc.createModel();
+
+ SbmlExporter sbmlExporter = new SbmlExporter();
+ Layout layout = sbmlExporter.createSbmlLayout(new ModelFullIndexed(null), result);
+
+ exporter.setSbmlModel(result);
+ exporter.setLayout(layout);
+ return exporter;
+ }
+
+ @Test
+ public void testAddColors() {
+ SbmlBioEntityExporter<?, ?> exporter = createMockExporter();
+ ColorDefinition c1 = exporter.getColorDefinition(Color.BLUE);
+ ColorDefinition c2 = exporter.getColorDefinition(Color.BLUE);
+ assertEquals(c1, c2);
+ }
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
index 3d6832feedb6c3867094a78ff5189fd2f4412a5b..ad40790555de5aea076bce9db4f36e6f25e7dc42 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -5,15 +5,13 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
+import java.awt.Color;
import java.awt.Desktop;
import java.awt.geom.Point2D;
import java.io.ByteArrayInputStream;
import java.io.File;
-import java.io.InputStream;
-import java.io.StringWriter;
import java.nio.file.Files;
-import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
import org.junit.Test;
@@ -23,17 +21,18 @@ import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
import lcsb.mapviewer.converter.graphics.PngImageGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
@@ -42,6 +41,8 @@ public class SbmlExporterTest {
SbmlParser parser = new SbmlParser();
SbmlExporter exporter = new SbmlExporter();
+ ModelComparator comparator = new ModelComparator();
+
@Test
public void testExportCompartment() throws Exception {
Model model = getModelAfterSerializing("testFiles/layoutExample/CompartmentGlyph_Example_level2_level3.xml");
@@ -67,6 +68,7 @@ public class SbmlExporterTest {
private Model getModelAfterSerializing(Model originalModel) throws Exception {
String xml = exporter.toXml(originalModel);
+ logger.debug(xml);
ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
Model result = parser.createModel(new ConverterParams().inputStream(stream));
// showImage(originalModel);
@@ -261,7 +263,7 @@ public class SbmlExporterTest {
assertEquals(0, comparator.compare(model, model2));
}
-
+
@Test
public void testExportProblematicNotes() throws Exception {
Model model = createModelWithReaction();
@@ -274,4 +276,39 @@ public class SbmlExporterTest {
assertEquals(reaction.getNotes(), deserializedReaction.getNotes());
}
+
+ @Test
+ public void testColorParsing() throws Exception {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/example1.xml"));
+ for (Element element : model.getElements()) {
+ element.setColor(Color.BLUE);
+ }
+ Model model2 = getModelAfterSerializing(model);
+ assertEquals(0, comparator.compare(model, model2));
+ }
+
+ @Test
+ public void testReactionColorParsing() throws Exception {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/example1.xml"));
+ for (Reaction element : model.getReactions()) {
+ for (AbstractNode node: element.getNodes()) {
+ node.getLine().setColor(Color.BLUE);
+ }
+ }
+ Model model2 = getModelAfterSerializing(model);
+ assertEquals(0, comparator.compare(model, model2));
+ }
+
+ @Test
+ public void testReactionLineWidthParsing() throws Exception {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/example1.xml"));
+ for (Reaction element : model.getReactions()) {
+ for (AbstractNode node: element.getNodes()) {
+ node.getLine().setWidth(12.7);
+ }
+ }
+ Model model2 = getModelAfterSerializing(model);
+ assertEquals(0, comparator.compare(model, model2));
+ }
+
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
index 68625d82772a07831a96a6c6f2dae65b9b383c59..8f1cc44b8194b62c33423b5ec454f01dc07e24e1 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
@@ -5,11 +5,13 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
+import java.awt.Color;
import java.io.FileNotFoundException;
import org.apache.log4j.Logger;
import org.junit.Test;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -151,9 +153,35 @@ public class SbmlParserTest {
assertEquals(1, model.getCompartments().iterator().next().getMiriamData().size());
}
- @Test(expected=InvalidInputDataExecption.class)
+ @Test(expected = InvalidInputDataExecption.class)
public void testInvalidReactionLayout() throws Exception {
- parser.createModel(new ConverterParams().filename("testFiles/invalidReaction/reaction_with_missing_part_of_layout.xml"));
+ parser.createModel(
+ new ConverterParams().filename("testFiles/invalidReaction/reaction_with_missing_part_of_layout.xml"));
+ }
+
+ @Test
+ public void testDefaultColors() throws Exception {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/small/default_colors.xml"));
+ assertNotNull(model);
+ assertEquals(Color.BLUE, model.getElementByElementId("Species_1").getColor());
+ assertEquals(Color.RED, model.getElementByElementId("Species_2").getColor());
+
+ Reaction r1 = null;
+ Reaction r2 = null;
+ for (Reaction reaction : model.getReactions()) {
+ if (reaction.getElementId().contains("Reaction_1")) {
+ r1 = reaction;
+ }
+ if (reaction.getElementId().contains("Reaction_2")) {
+ r2 = reaction;
+ }
+ }
+ assertEquals(Color.BLUE, r1.getReactants().get(0).getLine().getColor());
+ assertEquals(3.0, r1.getReactants().get(0).getLine().getWidth(), Configuration.EPSILON);
+
+ assertEquals(Color.GREEN, r2.getReactants().get(0).getLine().getColor());
+ assertEquals(2.0, r2.getReactants().get(0).getLine().getWidth(), Configuration.EPSILON);
+
}
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
index 8aa572c29da12bc2942babdbc85ab5b7dd88c0ee..a3ed722dd9f0e8e8ac8a43b54718feb80bac05f5 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
@@ -6,9 +6,9 @@ import org.apache.log4j.Logger;
import org.junit.Test;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.ext.layout.Layout;
-import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
+import lcsb.mapviewer.converter.model.sbml.SbmlExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
@@ -51,7 +51,7 @@ public class SbmlSpeciesExporterTest {
Element protein2 = new GenericProtein("sa2");
protein2.setName("SNCA");
protein2.setCompartment(compartment);
-
+
Model model = new ModelFullIndexed(null);
model.addElement(protein1);
model.addElement(protein2);
@@ -68,10 +68,8 @@ public class SbmlSpeciesExporterTest {
SBMLDocument doc = new SBMLDocument(3, 1);
sbmlModel = doc.createModel(model.getIdModel());
- LayoutModelPlugin layoutPlugin = new LayoutModelPlugin(sbmlModel);
- sbmlLayout = new Layout();
- layoutPlugin.add(sbmlLayout);
- sbmlModel.addExtension("layout", layoutPlugin);
+ SbmlExporter sbmlExporter = new SbmlExporter();
+ sbmlLayout = sbmlExporter.createSbmlLayout(model, sbmlModel);
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(sbmlLayout, model);
compartmentExporter.exportElements(sbmlModel);
diff --git a/converter-sbml/testFiles/small/default_colors.xml b/converter-sbml/testFiles/small/default_colors.xml
new file mode 100644
index 0000000000000000000000000000000000000000..1a2bc53d9e6d113b8e54bdb773cef35c46843310
--- /dev/null
+++ b/converter-sbml/testFiles/small/default_colors.xml
@@ -0,0 +1,87 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" render:required="false" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
+ <model id="TestModel">
+ <layout:listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout id="Layout_1">
+ <render:listOfRenderInformation xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
+ <render:renderInformation>
+ <render:listOfStyles>
+ <render:style render:roleList="style_Compartment_1">
+ <render:g render:fill="color_FF0000FF"/>
+ </render:style>
+ </render:listOfStyles>
+ </render:renderInformation>
+ <render:renderInformation render:id="minerva_definitions">
+ <render:listOfColorDefinitions>
+ <render:colorDefinition render:id="blue_color" render:value="#0000FFFF"/>
+ <render:colorDefinition render:id="red_color" render:value="#FF0000FF"/>
+ <render:colorDefinition render:id="green_color" render:value="#00FF00FF"/>
+ </render:listOfColorDefinitions>
+ <render:listOfStyles>
+ <!-- element type specific -->
+ <render:style render:roleList="default_GenericProtein">
+ <render:g render:fill="blue_color"/>
+ </render:style>
+ <render:style render:roleList="default_SimpleMolecule">
+ <render:g render:fill="red_color"/>
+ </render:style>
+ <!-- reaction type specific -->
+ <render:style render:roleList="default_StateTransitionReaction">
+ <render:g render:fill="green_color" render:stroke-width="2.0"/>
+ </render:style>
+ <!-- element specific -->
+ <render:style render:roleList="style_Species_1">
+ <render:g render:fill="blue_color"/>
+ </render:style>
+ <!-- reaction specific -->
+ <render:style render:roleList="style_Reaction_1">
+ <render:g render:fill="blue_color" render:stroke-width="3.0"/>
+ </render:style>
+ </render:listOfStyles>
+ </render:renderInformation>
+ </render:listOfRenderInformation>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfCompartments>
+ <compartment id="Compartment_1" size="1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="Species_1" compartment="Compartment_1" initialConcentration="0"/>
+ <species id="Species_2" compartment="Compartment_1" initialConcentration="0"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="Reaction_1" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Species_1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Species_2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="Reaction_2" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Species_2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_3"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Species_1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_4"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/pom.xml b/pom.xml
index 947569cfae6e22e447d40af2a61e4c1d4ebf55ff..a8adf9f7c41337b1f9961934ab407e653af131da 100644
--- a/pom.xml
+++ b/pom.xml
@@ -54,6 +54,8 @@
<jaxb.version>2.2.7</jaxb.version>
<batik.version>1.8</batik.version>
+
+ <jsbml.version>1.4</jsbml.version>
<itext.version>5.5.6</itext.version>